All I can say is, its IE, what do you expect?
You could either examine the 'problematic' CSS where the alignment is defined to see if you can tweak the CSS to 'work' in all browsers or try a IE9 only stylesheet. I don't recommend the latter though.
IE9 supports CSS2.1 more fully than other browsers, so the issue isn't in IE9 by logic. You don't have to target IE9, at all. That's just poor practice. But we do need a link to the webpage in question or examples to be able to help more.